The ubiquitin-proteasome system (UPS) is a selective proteolysis pathway. In the UPS, a cellular protein, after being modified by polyubiquitylation, is targeted to the proteasome for proteolysis. Polyubiquitylation is a posttranslational modification process that requires a member of the ubiquitin-conjugating enzymes (also known as E2 enzymes), which works in concert with a member of the ubiquitin protein ligases (also known as E3 enzymes). E2 carries an activated ubiquitin as a thiolester complex (E2˜Ub) and docks onto E3, which contains a substrate protein binding site, and successive transfer of the ubiquitin in E2˜Ub to the E3-bound substrate leads to polyubiquitylation of a substrate protein. In this process, the discharged E2 leaves after each cycle and is reconverted into the E2˜Ub form through the action of the ubiquitin-activating enzyme (also known as E1). For the targeting of a protein to the proteasome, this polyubiquitination requires the formation of a polyubiquitin chain in which the K48 residue in ubiquitin serves as the linkage for ubiquitin chain elongation. Other forms of polyubiquitin linkages (K29, K11 and K63) are also found, and these polyubiquitin chains are used for other functions unrelated to UPS.
Protein degradation via UPS serves a wide range of important functions, some of which are essential for cell and animal survival. This process is used in the regulation of many gene transcription events in response to environmental changes. For example the activation of NFkB in inflammatory response is mediated by the selective degradation of IkB, and the selective degradation of HIF1 provides a means to exercise control on the transcription of genes under hypoxia. Other examples are provided by cell cycle transition and checkpoint controls where the expression of specific regulatory proteins is regulated in part by their selective degradation via UPS. UPS is also used in protein quality control in which misfolded or damaged proteins can be selectively removed by degradation.
There is a continuing need for compositions and methods for identifying modulators of UPS mediated protein degradation.